_pkgdown.yml

url: ~
template:
  bootstrap: 5

home:
  title: An R package for analysis of High Throughput Phenotyping data

navbar:
  title: "statgenHTP"
  left:
    - icon: fa-home
      href: index.html
    - text: "Vignettes"
      href: articles/index.html
  right:
    - icon: fa-newspaper-o
      text: "news"
      href: news/index.html
    - icon: fa-file-code-o
      text: "functions"
      href: reference/index.html
    - icon: fa-seedling
      text: "other packages"
      menu:
        - text: "statgenSTA"
          href: https://biometris.github.io/statgenSTA
        - text: "statgenGxE"
          href: https://biometris.github.io/statgenGxE
        - text: "statgenGWAS"
          href: https://biometris.github.io/statgenGWAS
        - text: "statgenQTLxT"
          href: https://biometris.github.io/statgenQTLxT
        - text: "statgenIBD"
          href: https://biometris.github.io/statgenIBD
        - text: "statgenMPP"
          href: https://biometris.github.io/statgenMPP
        - text: "LMMsolver"
          href: https://biometris.github.io/LMMsolver
    - icon: fa-github fa-lg fab
      text: "github"
      href: https://github.com/Biometris/statgenHTP

articles:
  - title: "Vignettes"
    desc: >
      The vignettes provide a full description of the statgenHTP package
      including some fully worked examples.
    contents:
      - Overview_HTP
      - vignettesSite/Intro_HTP
      - vignettesSite/OutlierSingleObs_HTP
      - vignettesSite/SpatialModel_HTP
      - vignettesSite/OutlierSerieObs_HTP
      - vignettesSite/HierarchicalDataModel_HTP
      - vignettesSite/ParameterEstimation_HTP

reference:
- title: Data preparation
- contents:
  - createTimePoints
  - plot.TP
  - summary.TP
  - getTimePoints
  - removeTimePoints
  - as.data.frame.TP
- title: Detect outliers for single observations
- contents:
  - detectSingleOut
  - removeSingleOut
  - plot.singleOut
  - detectSingleOutMaize
- title: Spatial modeling
- contents:
  - fitModels
  - plot.fitMod
  - summary.fitMod
  - getGenoPred
  - getCorrected
  - getHerit
  - getVar
  - getEffDims
- title: Fit splines
- contents:
  - fitSpline
  - plot.HTPSpline
- title: Estimate parameters
- contents:
  - estimateSplineParameters
  - plot.splineEst
- title: Fit HDM splines
- contents:
  - fitSplineHDM
  - predict.psHDM
  - plot.psHDM
- title: Detect outliers for series of observations
- contents:
  - detectSerieOut
  - removeSerieOut
  - plot.serieOut
- title: Example data
- contents:
  - PhenoarchDat1
  - PhenovatorDat1
  - RootDat1
  - spatCorrectedArch
  - spatCorrectedVator
  - noCorrectedRoot
  - spatPredArch
- title: Utility functions
- contents:
  - countValid
  - countValidPlot